Hi Poornima,<br>If you can paste the entire mdp file, then it can be easy for the users to suggest you things.<br>Cheers,<br><br><div><span class="gmail_quote">On 3/31/06, <b class="gmail_sendername">poornima Gajendrarao</b>
<<a href="mailto:poornings@yahoo.co.in">poornings@yahoo.co.in</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear Bruce,
<br><br>Thank you very much for your suggestion.<br><br>I tried as you said. But the only difference Which I<br>saw is that the temperautre goes upto 314 (I tried it<br>with 10ps MDrun). After that I tried for 100ps MDrun.
<br>I used the same parameters which you have mentioned in<br>the previous mail. I didnt change anything. And while<br>running the grompp program for simulated annealing..<br><br>I am getting these warnings:<br><br>ARNING 1 [file
full.mdp, line unknown]:<br> Unknown left-hand coulomb type in parameter file<br><br>WARNING 2 [file full.mdp, line unknown]:<br> Unknown left-hand anneaing in parameter file<br><br>WARNING 3 [file full.mdp, line unknown]:
<br> Unknown left-hand anneling_npoints in parameter file<br><br>can any one help to solve this problem!!<br><br>Thanks in advance.<br><br>with prayers,<br>Poornima<br><br><br><br><br><br>--- <a href="mailto:bfmilne@ff.up.pt">
bfmilne@ff.up.pt</a> wrote:<br><br>> Hi Poornima,<br>><br>> It could be that you are defining two<br>> energy/temperature groups:<br>> >tc-grps = Protein SOL<br>> >tau_t = 0.1 0.1<br>> >ref_t = 300 300
<br>> >; Energy monitoring<br>> >energygrps = Protein SOL<br>><br>> but then only defining annealing protocols for one<br>> group:<br>> >;simulated annealing<br>> >anneling = single<br>> >anneling_npoints = 5
<br>> >anneling_time = 2 4 6 8 10<br>> >anneling_temp = 320 338 350 360 370<br>><br>> I think it should be like this:<br>><br>> annealing = single single<br>> annealing_npoints = 5 5<br>> annealing_time = 2 4 6 8 10 2 4 6 8 10
<br>> annealing_temp = 320 338 350 360 370 320 338 350 360<br>> 370<br>><br>> Have a look at the mdp options part of the online<br>> manual and check the SA part.<br>><br>> Cheers,<br>><br>> Bruce
<br>><br>> --<br>> Dr. Bruce F. Milne PhD<br>> CEQOFFUP<br>> Faculdade de Farmácia<br>> Universidade do Porto<br>> Rua Aníbal Cunha - 164<br>> 4050-047<br>> Porto<br>> Portugal<br>><br>>
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